Tools and services documentation

Version 2.1 by graber on 2021/04/22 09:24
               
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 [ fairgraph 0.5.1](https://fairgraph.readthedocs.io/en/latest/)  [3D Slicer 4.10.2](https://www.slicer.org/wiki/Documentation/4.10)  
 [3D Structure Tensor Analysis ](https://github.com/lens-biophotonics/st_fibre_analysis_hbp)  [3DSlicer 4.10.1](https://github.com/Slicer/Slicer)  [3DSpineMFE 1.0_RC4](https://github.com/ComputationalIntelligenceGroup/3DSpineMFE/blob/master/README.md)  
 [3DSpineS 0.1](https://github.com/ComputationalIntelligenceGroup/3DSpineS/blob/master/README.Rmd)  [3DSynapsesSA 1.2](https://neurosuites.com/static/neurosuite/docs/3DSynapsesSA/3DSynapsesSA_users_guide_v1.1.pdf)  [Android app for multimodal data acquisition from wearables 1.0](https://c4science.ch/diffusion/9555/browse/master/README.md)  
 [Arbor v0.2.2](https://arbor.readthedocs.io/en/latest/index.html)  [Arbor v0.5](https://arbor.readthedocs.io/en/v0.5/)  [BasalUnit 1.0.4](#)  
 [Bids Manager & Pipeline 0.2.5](https://github.com/Dynamap/BIDS_Manager)  [BluePyMM 0.6.65](https://bluepymm.readthedocs.io/en/latest/index.html)  [BluePyOpt 1.9.3](https://bluepyopt.readthedocs.io/en/latest/)  
 [Brain Simulation Platform Service Account 1.0.0](https://humanbrainproject.github.io/hbp-bsp-service-account/)  [Brayns 1.0.0](http://bluebrain.github.io/Brayns-1.0/index.html)  [Brion 3.2.0](#)  
 [Central Nervous System bioactive compounds beta](#) [ChemBioServer 2](https://chembioserver.vi-seem.eu/Tutorial.php)  [Clint Explorer 0.1](https://gmrv.es/gmrvvis/clintexplorer/)  
 [Connectivity-based Psychometric Prediction Framework 1.1](https://github.com/inm7/cbpp/blob/master/README.md)  [Connectomic Composition Predictor (2020-03-03)](https://github.com/ntimonid/Connectomic-Composition-Predictor-CCP-/blob/master/PrimaryLibrary.ipynb)  [CoreNeuron 0.16](https://github.com/BlueBrain/CoreNeuron)  
 [Cube 4.4.4](https://apps.fz-juelich.de/scalasca/releases/cube/4.4/docs/guide/html/)  [CxSystem2 1.0](https://cxsystem2.readthedocs.io/en/latest/)  [DC Explorer 1.0](#)  
 [Data Catalogue 1.6.0](https://github.com/LREN-CHUV/data-catalog-setup/blob/master/README.md)  [Demics 1.0.0-alpha](https://github.com/FZJ-INM1-BDA/demics/blob/master/README.md)  [EBRAINS Knowledge Graph v2.3 ](https://kg.ebrains.eu/)  
 [Elephant 0.6.4](https://elephant.readthedocs.io/en/v0.6.4/index.html)  [Elephant 0.7.0](https://elephant.readthedocs.io/en/latest/index.html)  [Event-Based Heart Rate Estimation from ECG Signals 1.0](https://c4science.ch/source/Event_based_gQRS/browse/master/README.md)  
 [ExploreASL 1.3.0](https://docs.google.com/document/d/10OpHiXTxDUtNar-FAQQeq9unS9j0zC4y0X86okK0t_U/edit#heading=h.gjdgxs)  [Extra-P 3.0](https://www.scalasca.org/scalasca/software/extra-p/documentation.html)  [Extrae 3.7.1](https://tools.bsc.es/doc/html/extrae/index.html)  
 [FAConstructor 1.7.0](https://iffmd.fz-juelich.de/s/HJTaAO9aN#)  [Factorisation-based Image Labelling 0.1.1](#)  [Feature Extraction Graphical User Interface 1.4](https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/trace_analysis/efel_gui/efel_gui.html)  
 [Frites - Framework for information theoretical analysis of electrophysiological data and statistics 0.3.8](https://brainets.github.io/frites/index.html)  [Gabaclassifier 1.0](https://github.com/ComputationalIntelligenceGroup/gabaclassifier/blob/master/README.md)  [Ginkgo/GlobalTractography](#)  
 [Ginkgo/MEDUSA 1.0](#) [HBP Validation Framework - Python Client 0.5.28](http://hbp-validation-client.readthedocs.io/)  [HiBoP 2.2.3a](https://collab.humanbrainproject.eu/#/collab/78584/nav/531987?state=uuid%3Df72e40d9-a0bf-4ab7-8a27-462911107c5f)  
 [HippoUnit 1.3.5](https://hippounit.readthedocs.io/)  [Hodgkin Huxley Neuron Builder 1.3.0](https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/single_cell_building/hippocampus/p1_hh_neuron_builder/p1_hh_neuron_builder.html)  [Human Brain Project HPC Status Monitor 1.0.0](https://humanbrainproject.github.io/hbp-sp6-guidebook/hpc_status_monitor/hpc_status_monitor.html#)  
 [ImageJ 2.0.0-rc-71](https://github.com/imagej/imagej)  [ImageJ 2.0.0-rc-72](https://github.com/imagej/imagej/blob/master/README.md)  [InDiProv 2.0](https://github.com/HBPVIS/InDiProv/blob/master/README.md)  
 [Insite beta](https://vrgrouprwth.github.io/insite/)  [Interactive Atlas Viewer 2.2.3](https://interactive-viewer.readthedocs.io/en/latest/)  [JuGEx 1.0](https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html)  
 [JupyterLab v1.2.4](https://jupyterlab.readthedocs.io/en/stable/index.html)  [KnowledgeSpace v3.0.0](https://knowledge-space.org/documentation)  [LePetitPrince 0.01a](#)  
 [Lempel Ziv Perturbational Complexity Index 1.0](https://github.com/iTCf/PCIcalc)  [Livre 0.8.0](https://bluebrain.github.io/Livre-0.8/index.html)  [LocaliZoom 0.9](https://collab.humanbrainproject.eu/#/collab/5401/nav/42133)  
 [MIP Microservice Infrastructure 4.0.2](https://github.com/HBPMedical/mip-microservices-infrastructure/tree/master/docs)  [MRIcroGL v1.2.20200331](https://www.nitrc.org/plugins/mwiki/index.php/mricrogl:MainPage)  [MRIcron v1.0.20190902](https://people.cas.sc.edu/rorden/mricron/index.html)  
 [MRtrix3 3.0.2](https://mrtrix.readthedocs.io/en/3.0.2/)  [MRtrix3_connectome 0.4.2](https://github.com/BIDS-Apps/MRtrix3_connectome/blob/0.4.2/README.md)  [MSPViz v0.2.6](https://github.com/gmrvvis/MSPViz/blob/master/README.md)  
 [MeLVin 1.0](https://www.youtube.com/watch?v=-gNbR7fnV9Q)  [MeshView 0.9](https://www.nitrc.org/plugins/mwiki/index.php/meshview:MainPage)  [MorphoUnit 1.0.4](#)  
 [Multi-Brain 0.1.0](https://github.com/WTCN-computational-anatomy-group/diffeo-segment/blob/v0.1.0/manual-mb.pdf)  [Multi-scale brain simulation with TVB-NEST 1.0.1](https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs)  [NEST Desktop 2.4.1](https://nest-desktop.readthedocs.io)  
 [NEST Desktop 2.5.0](https://nest-desktop.readthedocs.io)  [NEST Instrumentation  App 0.3](https://github.com/compneuronmbu/NESTInstrumentationApp/blob/master/README.md)  [NEST v2.20.0](https://nest-simulator.readthedocs.io/en/v2.20.0/)  
 [NESTML 3.1](https://nestml.readthedocs.io/en/latest/)  [NEURON 7.7.2](https://www.neuron.yale.edu/neuron/docs)  [NMODL Framework 0.2](https://bluebrain.github.io/nmodl/html/index.html)  
 [NSuite 1.0](https://nsuite.readthedocs.io/en/latest/index.html)  [Nehuba - Online visualization of large volumetric brain images alpha](https://github.com/HumanBrainProject/nehuba)  [Neo 0.8.0](https://neo.readthedocs.io/en/stable/)  
 [Neo Viewer 1.0.0](https://neo-viewer.brainsimulation.eu/)  [NetPyNE 0.9.5](http://www.netpyne.org/index.html)  [NetPyNE GUI 0.5.2](https://github.com/MetaCell/NetPyNE-UI/wiki)  
 [NetworkUnit 0.1.1](https://github.com/INM-6/NetworkUnit)  [NeuroM 1.4.17](https://neurom.readthedocs.io/en/v1.4.17/)  [NeuroSTR 0.1](https://computationalintelligencegroup.github.io/neurostr/doc/)  
 [NeuroScheme 0.3](https://neuroscheme-documentation.readthedocs.io/en/latest/)  [NeuroSuites 1.0](https://gitlab.com/mmichiels/neurosuite/-/tree/master/documentation)  [NeuroTessMesh 0.0.1](https://neurotessmesh-documentation.readthedocs.io/en/latest/)  
 [Neurolucida 2019](#) [Neurolucida Version 2020.1.3](#)  [Neuromorphic Platform Python client 0.8.2](https://electronicvisions.github.io/hbp-sp9-guidebook/)  
 [Neuron Segmentation Tool](https://github.com/lens-biophotonics/neuron_segmentation_model_hbp/tree/master/tensorflow_2.5D_model)  [Neuronize 2.0.0](https://docs.google.com/document/d/1wgXFyhbiehLDr7nEg-jvb9HlIiybbW7U0OCjRGzgWj0/edit?usp=sharing)  [Neurorobotics Platform 3.0](https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html)  
 [Nilearn 0.5.2](http://nilearn.github.io/user_guide.html)  [Nilearn 0.6.2](http://nilearn.github.io/user_guide.html)  [Nutil 0.33](https://www.nitrc.org/plugins/mwiki/index.php/nutil:MainPage)  
 [Nutil 0.403](https://wiki.ebrains.eu/bin/view/Collabs/quint)  [ODE-toolbox v2.0](https://ode-toolbox.readthedocs.io/en/master/)  [OTF2 2.2](http://perftools.pages.jsc.fz-juelich.de/cicd/otf2/docs/otf2-2.2/html/)  
 [PLIViewer 1.2.0](https://devhub.vr.rwth-aachen.de/VR-Group/pli_vis/blob/master/readme.md)  [ParaView 5.8.0](https://www.paraview.org/documentation/)  [Paraver 4.8.2](https://tools.bsc.es/doc/1364.pdf)  
 [PoSCE 0.1a](#)  [PyJuGex 1.0.1alpha](https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html)  [PyNN 0.9.5](http://neuralensemble.org/docs/PyNN/)  
 [PyramidalExplorer 0.2.0](https://gmrv.es/pyramidalexplorer/)  [QuickNII v2.2](https://www.nitrc.org/docman/?group_id=1341)  [RTNeuron 3.0](https://bluebrain.github.io/RTNeuron-3.0/index.html)  
 [ReMoToo 0.0.2](https://github.com/vg-lab/ReMoToo/blob/v0.0.2/README.md)  [Remote Connection Manager 1.2](https://wiki.u-gov.it/confluence/pages/viewpage.action?pageId=324275042)  [SCAIView-NEURO-2020](https://www.scaiview.com/en/first-steps.html)  
 [SDA: Simulation of Diffusional Association 7.2.4](https://mcm.h-its.org/sda/doc/doc_sda7/doc.html)  [SLURM plugin for the co-allocation of compute and data resources v1.0](https://github.com/HumanBrainProject/coallocation-slurm-plugin/blob/master/README.md)  [SNT 3.1.105](https://imagej.net/SNT)  
 [Scalasca 2.5](https://apps.fz-juelich.de/scalasca/releases/scalasca/2.5/docs/UserGuide.pdf)  [Score-P 6.0](http://scorepci.pages.jsc.fz-juelich.de/scorep-pipelines/docs/scorep-6.0/html/)  [Single Cell Model Builder Notebook 1.1](https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/single_cell_building/hippocampus/build_scm_hbp/build_scm_hbp.html)  
 [Single Cell Model Rebuilder Notebook 1.1](https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/single_cell_building/hippocampus/rebuild_existing/rebuild_scm.html)  [SpectralSegmentation 1.0](https://github.com/Leveltlab/SpectralSegmentation/blob/master/README.md)  [SpykeViewer 0.4.2](https://spyke-viewer.readthedocs.io/en/latest/index.html)  
 [Surf Ice v1.0.20190902](https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage)  [Synaptic events fitting Notebook 1.3](https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/trace_analysis/syn_events_fit/syn_events_fit.html#synaptic-events-fitting)  [Synaptic plasticity 0.1](https://collab.humanbrainproject.eu/#/collab/1655/nav/18580)  
 [TVB Brain Atlas Viewer 1.0](#) [TVB image processing pipeline 1.0](https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view)  [TVB-HPC v1.0-beta](https://github.com/the-virtual-brain/tvb-hpc/tree/master/docs)  
 [The Jupyter Notebook 6.0.2](https://jupyter-notebook.readthedocs.io/en/stable/)  [The Virtual Brain 1.5.8](http://docs.thevirtualbrain.org/index.html)  [The Virtual Brain Web-App 2.0.6](http://docs.thevirtualbrain.org/)  
 [The fast and parallel Virtual Brain 1.0](https://collab.humanbrainproject.eu/#/collab/65304/nav/444404)  [Threading Building Blocks 2019 Update 9](https://software.intel.com/en-us/tbb/documentation)  [Tide 1.5.0](https://bluebrain.github.io/Tide-1.5/index.html)  
 [UG4 4.3.1](http://ug4.github.io/docs/)  [Unicore 8.0.0](https://www.unicore.eu/documentation/)  [VIOLA 2020-01-31](https://github.com/HBPVIS/VIOLA/wiki/VIOLA-User-Manual)  
 [VTK 8.2.0](https://www.kitware.com/products/books/VTKUsersGuide.pdf)  [VTK-m 1.5.0](http://m.vtk.org/images/c/c9/VTKmUsersGuide-1-5.pdf)  [Vaa3D v3.597](https://github.com/Vaa3D/Vaa3D_Wiki/wiki/Vaa3D-Wiki)  
 [Vaa3D v3.601](https://github.com/Vaa3D/Vaa3D_Wiki/wiki/Vaa3D-Wiki)  [ViSimpl 0.1.3](https://visimpl-documentation.readthedocs.io/en/latest/)  [Vishnu 1.0](https://gmrv.es/gmrvvis/vishnu/)  
 [VoluBA (04.01.2020)](https://voluba-user-doc.apps-dev.hbp.eu/)  [Woken 3.0.2](https://github.com/HBPMedical/woken/blob/master/README.md)  [ZetaStitcher 0.5.0](https://lens-biophotonics.github.io/ZetaStitcher/)  
 [deNEST 1.0.1](https://denest.readthedocs.io/en/latest/)  [eFEL 3.0](https://efel.readthedocs.io/en/latest/installation.html#installing-the-c-standalone-library)  [eFELunit 1.1.5](https://github.com/appukuttan-shailesh/eFELunit)  
 [fMRIPrep 20.1.1](https://fmriprep.org/en/stable/)  [fastPLI 0.9.8](https://github.com/3d-pli/fastpli/wiki)  [fmralign 0.0.1](https://parietal-inria.github.io/fmralign-docs/)  
 [hbp-spatial-backend 0.1.0.dev0](https://hbp-spatial-backend.apps.hbp.eu/redoc)  [ilastik 1.3.3](http://ilastik.org/documentation/index.html)  [multipipsa 4.0.2](#)  
 [neurostr 1.0](https://github.com/ComputationalIntelligenceGroup/neurostrr)  [notebooks_review2019](https://github.com/mb-BCA/notebooks_review2019)  [openMINDS metadata for TVB-ready data 1](#)  
 [pyGAlib 1.1.0](https://github.com/gorkazl/pyGAlib/blob/master/README.md)  [pyJUSBB 0.0.1](https://github.com/shahrzadkh/pyJUSBB/wiki)